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Crystal structure of a putative racemase with Mg ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MKC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 290 0.15M DL-Malic acid, 20% PEG 3350, 20mM Magnesium Chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.55 51.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.144 α = 90 b = 165.408 β = 90 c = 165.666 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2010-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 50 100 0.074 0.074 10.4 14.8 122663 22.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 100 0.435 0.435 7 14.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MIR THROUGHOUT 3MKC 2 50 118456 118456 4808 97.1 0.221 0.221 0.2146 0.244 0.2365 RANDOM 25.2
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.629 1.782 -0.153
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.612 c_scbond_it 2.042 c_mcangle_it 1.681 c_angle_deg 1.2 c_mcbond_it 1.143 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.612 c_scbond_it 2.042 c_mcangle_it 1.681 c_angle_deg 1.2 c_mcbond_it 1.143 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11798 Nucleic Acid Atoms Solvent Atoms 378 Heterogen Atoms 38
Software Software Software Name Purpose CBASS data collection MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling